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- PDB-3qjm: Structural flexibility of Shank PDZ domain is important for its b... -

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Basic information

Entry
Database: PDB / ID: 3qjm
TitleStructural flexibility of Shank PDZ domain is important for its binding to different ligands
Components
  • Beta-PIX
  • SH3 and multiple ankyrin repeat domains protein 1
KeywordsPROTEIN BINDING / PDZ domain / Protein-protein interaction / Beta-PIX
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / ankyrin repeat binding / regulation of AMPA receptor activity / dendritic spine morphogenesis / adult behavior / positive regulation of dendritic spine development / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / G protein-coupled receptor binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / SH3 domain binding / signaling receptor complex adaptor activity / scaffold protein binding / protein-containing complex assembly / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.311 Å
AuthorsLee, J.H. / Park, H. / Park, S.J. / Kim, H.J. / Eom, S.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
Authors: Lee, J.H. / Park, H. / Park, S.J. / Kim, H.J. / Eom, S.H.
History
DepositionJan 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 1
B: SH3 and multiple ankyrin repeat domains protein 1
C: Beta-PIX
D: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)26,6934
Polymers26,6934
Non-polymers00
Water1,44180
1
A: SH3 and multiple ankyrin repeat domains protein 1
C: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,3462
Polymers13,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-3 kcal/mol
Surface area6030 Å2
MethodPISA
2
B: SH3 and multiple ankyrin repeat domains protein 1
D: Beta-PIX


Theoretical massNumber of molelcules
Total (without water)13,3462
Polymers13,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-3 kcal/mol
Surface area6240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.625, 57.625, 144.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-60-

HOH

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Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 1 / Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / ...Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / SSTR-interacting protein / SSTRIP / Synamon


Mass: 12755.696 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WV48
#2: Protein/peptide Beta-PIX


Mass: 590.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM sodium acetate(pH 5.5-6.0), 0.8M lithium sulfate, 0.7M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 10106 / Num. obs: 10106 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 83.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.311→25.368 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8143 / SU ML: 0.25 / σ(F): 2.47 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 504 5 %RANDOM
Rwork0.2346 ---
obs0.2362 10087 89.48 %-
all-10106 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.148 Å2 / ksol: 0.418 e/Å3
Displacement parametersBiso max: 74.85 Å2 / Biso mean: 25.9547 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.4461 Å20 Å2-0 Å2
2--5.4461 Å20 Å2
3----10.8923 Å2
Refinement stepCycle: LAST / Resolution: 2.311→25.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 0 80 1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081631
X-RAY DIFFRACTIONf_angle_d1.1352193
X-RAY DIFFRACTIONf_chiral_restr0.071251
X-RAY DIFFRACTIONf_plane_restr0.005282
X-RAY DIFFRACTIONf_dihedral_angle_d16.631608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3105-2.54290.2931160.22492200231685
2.5429-2.91040.29651240.23742378250290
2.9104-3.6650.23881320.22122499263194
3.665-25.36940.26261320.23462506263889

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